Ubiquitin genes in Tetrahymena pyriformis and their expression during heat shock

Variations and evolution of polyubiquitin genes from ciliates

Polyubiquitin genes from seven ciliate species were amplified, cloned and sequenced. It is estimated that Strombidium sulcatum, Euplotes vannus, E. rariseta and Anteholosticha manca have a polyubiquitin gene of 3 repeats, and A. parawarreni, Paramecium caudatum and Pseudokeronopsis flava 4 repeats. The newly obtained ubiquitins mostly differ from that of humans by 1-5 residues in amino acid sequences. A neighbor-joining tree constructed based on monomeric ubiquitin genes supports the monophyly of an assemblage comprising the litostomateans and some oligohymenophoreans, but not the class Spirotrichea. The monomers from the same species are generally placed together and highly supported for the class Litostomatea, the genera Paramecium and Ichthyophthirius, but not for other species. The non-synonymous/synonymous rate ratio (dN/dS) at the protein level are less than 1, and the synonymous nucleotide differences per synonymous site (p(S)) from intraspecific comparisons are fairly high (0.02-0.72). These results indicate that ciliates have not only the conserved, but also some quite divergent, polyubiquitin genes and confirm that the polyubiquitin genes in ciliates evolve according to the birth-and-death mode of evolution under strong purifying selection.

Microtubule cytoskeleton perturbation induced by taxol and colchicine affects chaperonin containing TCP-1 (CCT) subunit gene expression in Tetrahymena cells

We report the existence of a CCT epsilon subunit gene that encodes subunit epsilon of the chaperonin CCT (chaperonin containing TCP-1) in Tetrahymena pyriformis. This work focuses on the study of the effects of the microtubule polymerizing agent taxol and the depolymerizing agent colchicine on microtubule dynamics and their role in the regulation of tubulin and CCT subunit genes. Under taxol treatment some TpCCT and tubulin genes are distinctly expressed until 30 min of treatment. Cytoplasmic TpCCT mRNA levels slightly decrease while tubulin transcripts are increasing. In colchicine treated cells TpCCT and tubulin transcripts decrease in the initial 30 min of treatment and then start to increase. However, both antimitotic agents induce TpCCT and tubulin gene transcription. This induction does not correlate with increased steady-state levels of TpCCT proteins and seems to be necessary to replete cytoplasmic TpCCT mRNAs. Moreover, we found that TpCCT epsilon and TpCCT alpha but not TpCCT eta are present in the insoluble fraction after a postmitochondrial fractionation that contains components of the ciliate cortex structure, basal bodies and cilia. This suggests that some TpCCT subunits may be associated with these structures. The association of TpCCT epsilon subunit is stimulated either by taxol or colchicine treatment. These observations support the idea that CCT subunits could have additional roles in vivo.

Cadmium metallothionein gene of Tetrahymena pyriformis

A genomic sequence from Tetrahymena pyriformis, encoding a cadmium-induced metallothionein has been cloned. The gene encodes a transcript of 487 bases, with an intronless coding region of 324 nt, using TGA as the stop codon, TAA coding for glutamine, and the translational initiation sequence AAAATGG. Two regions of internal similarity in the coding sequence support the hypothesis that the Tetrahymena protein arose by gene duplication. The sequences of untranslated regions show some similarities with nematode MT-1 and MT-2 transcripts. Sequence of 525 bases upstream of the transcription start contains a TATA box, a CAAT box reverse complement, and many short stretches partially matching the AP-1 and ACE-1 binding sites, but no characteristic sequences found in other metallothionein promoters.

Characterization of a polyubiquitin gene in T. thermophila and of ubiquitin gene expression during sexual reproduction and under stress conditions

A 5-unit polyubiquitin gene, TTU3, was isolated from a T. thermophila genomic library and sequenced. This gene presents an extra triplet coding for Phe, a AGAGA motif and a putative HSE element in its 5'-non-coding region. The ubiquitin gene expression in this ciliate was investigated by Northern blot hybridization in conjugating cells or cells under stress conditions. Exponentially growing cells express two ubiquitin mRNAs of 0.75 and 1.8 kb and a new species of 1.4 kb is induced under hyperthermic stress. During sexual reproduction of the cells (conjugation) the 1.8-kb mRNA is still transcribed whereas the steady-state population of the 0.75 mRNA transcripts is strongly diminished. Southern blot analysis suggests that ubiquitin in T. thermophila constitutes a large family of about ten members.

Characterization of the polyubiquitin gene in the marine red alga Gracilaria verrucosa

We have cloned a nuclear gene (UBI6R) and corresponding cDNAs that encode polyubiquitin in the florideophycidean red alga Gracilaria verrucosa. The gene encodes a polyubiquitin composed of six tandem ubiquitin units, followed by a single glutamine residue. The deduced amino acid sequences are identical among all six units, and identical to the ubiquitin of the florideophyte Aglaothamnion neglectum. There is high sequence similarity among the red algal ubiquitins and those of animals, green plants, fungi and several protists. Only one polyubiquitin gene was found by Southern hybridization analysis of G. verrucosa nuclear DNA. The upstream region of the gene is rich in putative cis-acting transcription-regulatory elements, including a putative heat-responsive element. Poly(A) addition to UBI6R mRNA was observed in cDNAs at four different sites, implicating the sequences AATAAA and (or) AGTAAA as poly(A) addition signals. The polyubiquitin genes of red algae show features of concerted evolution, but appear to be subject to less sequence homogenization than those of animals.

The DNA of ciliated protozoa

Ciliates contain two types of nuclei: a micronucleus and a macronucleus. The micronucleus serves as the germ line nucleus but does not express its genes. The macronucleus provides the nuclear RNA for vegetative growth. Mating cells exchange haploid micronuclei, and a new macronucleus develops from a new diploid micronucleus. The old macronucleus is destroyed. This conversion consists of amplification, elimination, fragmentation, and splicing of DNA sequences on a massive scale. Fragmentation produces subchromosomal molecules in Tetrahymena and Paramecium cells and much smaller, gene-sized molecules in hypotrichous ciliates to which telomere sequences are added. These molecules are then amplified, some to higher copy numbers than others. rDNA is differentially amplified to thousands of copies per macronucleus. Eliminated sequences include transposonlike elements and sequences called internal eliminated sequences that interrupt gene coding regions in the micronuclear genome. Some, perhaps all, of these are excised as circular molecules and destroyed. In at least some hypotrichs, segments of some micronuclear genes are scrambled in a nonfunctional order and are recorded during macronuclear development. Vegetatively growing ciliates appear to possess a mechanism for adjusting copy numbers of individual genes, which corrects gene imbalances resulting from random distribution of DNA molecules during amitosis of the macronucleus. Other distinctive features of ciliate DNA include an altered use of the conventional stop codons.

The Saccharomyces cerevisiae DNA repair gene RAD23 encodes a nuclear protein containing a ubiquitin-like domain required for biological function

In eukaryotes, the posttranslational conjugation of ubiquitin to various cellular proteins marks them for degradation. Interestingly, several proteins have been reported to contain ubiquitin-like (ub-like) domains that are in fact specified by the DNA coding sequences of the proteins. The biological role of the ub-like domain in these proteins is not known; however, it has been proposed that this domain functions as a degradation signal rendering the proteins unstable. Here, we report that the product of the Saccharomyces cerevisiae RAD23 gene, which is involved in excision repair of UV-damaged DNA, bears a ub-like domain at its amino terminus. This finding has presented an opportunity to define the functional significance of this domain. We show that deletion of the ub-like domain impairs the DNA repair function of RAD23 and that this domain can be functionally substituted by the authentic ubiquitin sequence. Surprisingly, RAD23 is highly stable, and the studies reported herein indicate that its ub-like domain does not mediate protein degradation. Thus, in RAD23 at least, the ub-like domain affects protein function in a nonproteolytic manner.

The Saccharomyces cerevisiae DNA repair gene RAD23 encodes a nuclear protein containing a ubiquitin-like domain required for biological function

In eukaryotes, the posttranslational conjugation of ubiquitin to various cellular proteins marks them for degradation. Interestingly, several proteins have been reported to contain ubiquitin-like (ub-like) domains that are in fact specified by the DNA coding sequences of the proteins. The biological role of the ub-like domain in these proteins is not known; however, it has been proposed that this domain functions as a degradation signal rendering the proteins unstable. Here, we report that the product of the Saccharomyces cerevisiae RAD23 gene, which is involved in excision repair of UV-damaged DNA, bears a ub-like domain at its amino terminus. This finding has presented an opportunity to define the functional significance of this domain. We show that deletion of the ub-like domain impairs the DNA repair function of RAD23 and that this domain can be functionally substituted by the authentic ubiquitin sequence. Surprisingly, RAD23 is highly stable, and the studies reported herein indicate that its ub-like domain does not mediate protein degradation. Thus, in RAD23 at least, the ub-like domain affects protein function in a nonproteolytic manner.

Clusters of 5S rRNAs in the intergenic region of ubiquitin genes in Tetrahymena pyriformis

Here, we report the molecular analysis of two independent 5S rRNA clusters found in the intergenic region of two ubiquitin genomic clones isolated from Tetrahymena pyriformis. Each cluster contains two 120-bp-long coding regions organized in tandem with 142/145-bp-long spacers.

Cloning of the polyubiquitin cDNA from the marine sponge Geodia cydonium and its preferential expression during reaggregation of cells

Ubiquitination of proteins is a critical step in the controlled degradation process of many polypeptides. Here we show that sponges, the simplest multicellular group of eukaryotic organisms, are also equipped with the ubiquitin pathway. The polyubiquitin cDNA was isolated and characterized from the marine sponge Geodia cydonium. The open reading frame contains six ubiquitin moieties, which are lined up head to tail without spacers. A comparison of the predicted amino acid sequence of the six sponge ubiquitin-coding units with those from other organisms revealed a high degree of homology (> 93%). The ubiquitin gene is expressed to almost the same extent in the two main compartments of the sponge, the cortex and the medulla. However, only in the cortex are detectable amounts of the ubiquitin protein synthesized. The ubiquitin protein isolated from the sponge organism was found to initiate protein degradation in the heterologous reticulocyte system in the same manner as bovine ubiquitin. In vitro studies with dissociated sponge cells revealed that the homologous aggregation factor causes (i) a strong increase in the steady-state level of mRNA coding for ubiquitin and (ii) a drastic increase in ubiquitin protein synthesis, while the homologous lectin failed to display that effect in isolated cells. These data suggest that ubiquitin may play a role in sponge morphogenesis.

Saccharomyces cerevisiae HSP70 heat shock elements are functionally distinct

The Saccharomyces cerevisiae HSP70 gene SSA1 has multiple heat shock elements (HSEs). To determine the significance of each of these sequences for expression of SSA1, we analyzed expression from a set of promoters containing point mutations in each of the HSEs, individually and in pairwise combinations. Of the three HSE-like sequences, two (HSE2 and HSE3) were active promoter elements; only one, HSE2, was active under basal growth conditions. Either HSE2 or HSE3 alone was able to drive SSA1 transcription at near-normal rates after heat shock. Both HSE2 and HSE3 were capable of driving basal transcription when placed in the context of the CYC1 promoter. Previous analysis had identified an upstream repressing sequence overlapping HSE2 that repressed basal transcription driven by HSE2. Our analysis showed that basal transcription driven by HSE3 was repressed both by the distant upstream repressing sequence and by closer flanking sequences. The ability to drive basal transcription is not inherent in all natural HSEs, since the HSEs from the heat-inducible SSA3 and SSA4 genes showed no basal activity when placed in the CYC1 vector. Gel mobility shift experiments showed that the same population of heat shock transcription factor molecules bound to HSEs capable of driving basal activity and to HSEs having very low or undetectable basal activity.

Saccharomyces cerevisiae HSP70 heat shock elements are functionally distinct

The Saccharomyces cerevisiae HSP70 gene SSA1 has multiple heat shock elements (HSEs). To determine the significance of each of these sequences for expression of SSA1, we analyzed expression from a set of promoters containing point mutations in each of the HSEs, individually and in pairwise combinations. Of the three HSE-like sequences, two (HSE2 and HSE3) were active promoter elements; only one, HSE2, was active under basal growth conditions. Either HSE2 or HSE3 alone was able to drive SSA1 transcription at near-normal rates after heat shock. Both HSE2 and HSE3 were capable of driving basal transcription when placed in the context of the CYC1 promoter. Previous analysis had identified an upstream repressing sequence overlapping HSE2 that repressed basal transcription driven by HSE2. Our analysis showed that basal transcription driven by HSE3 was repressed both by the distant upstream repressing sequence and by closer flanking sequences. The ability to drive basal transcription is not inherent in all natural HSEs, since the HSEs from the heat-inducible SSA3 and SSA4 genes showed no basal activity when placed in the CYC1 vector. Gel mobility shift experiments showed that the same population of heat shock transcription factor molecules bound to HSEs capable of driving basal activity and to HSEs having very low or undetectable basal activity.

Heat-shock-induced protein synthesis is responsible for the switch-off of hsp70 transcription in Tetrahymena

We had previously described that new RNA synthesis is required for expression of the heat shock protein HSP70. Here, we find that the HSP70 mRNA decreases its levels under stress conditions, heat shock (HS) or arsenite (As), and that its levels start to decline at the same time as maximal HSPs synthesis (including HSP70) occurs. This suggests that regulation of the hsp70 gene is mainly exerted at the transcriptional level. Accumulation of the HSP70 mRNA in cells stressed in presence of cycloheximide (CHX), indicates that (a) protein(s) non-existent before stress, possibly HSP70 itself (which is shown here to be relatively stable), is involved in negatively regulating hsp70 expression. Since degradation of the HSP70 mRNA is also shown to occur in cells heat-shocked under CHX, as seen from decay of its levels upon addition of actinomycin D (AMD), the protein(s) must repress hsp70 expression at the transcriptional level. Other conditions that affect normal protein synthesis, namely the translation inhibitor puromycin and the arginine-analog canavanine (shown here to be stress inducers in Tetrahymena pyriformis), also cause a delay in transcription-arrest of the HSP70 mRNA. Under severe stress conditions of HS (36 degrees C) or As (350 microM), the levels of HSP70 mRNA are higher than under mild stress conditions, however, no significant difference is seen in the pattern of HSP70 mRNA decay.

Ubiquitin found in the archaebacterium Thermoplasma acidophilum

Systematic N-terminal sequencing of the low molecular weight proteins from Thermoplasma acidophilum separated by two-dimensional poly-acrylamide gel electrophoresis led to the discovery of a polypeptide with an apparent M(r) of 4.5 kDa identical as its first 18 amino acid residues to human ubiquitin. The occurrence of ubiquitin and proteasomes in an archaebacterium strongly suggests that ATP-ubiquitin-dependent proteolysis is a cellular function that developed early in evolution.

Synthesis and secretion of low molecular weight cuticular proteins during heat shock in the tobacco hornworm, Manduca sexta

In the tobacco hornworm, Manduca sexta, heat shock normally elicits synthesis of the classic heat-shock proteins. A 1-hr heat shock of 42 degrees C and above can also increase the relative synthesis of certain 12-18 kD proteins in the epidermis. These 12-18 kD proteins were identified as cuticular proteins for several reasons. Like cuticular proteins, they appear only in the epidermis. They can be precipitated from epidermal homogenates with an antiserum to larval cuticle. The same conditions that increased labeled 12-18 kD proteins in the epidermis also increased labeled 12-18 kD proteins in the cuticle. Some of the epidermal increase may result from a partial inhibition of secretion to the cuticle during 46 degrees C heat shock, causing abnormal accumulation in the epidermis. However, slight increases also occur at lower temperatures, which do not inhibit secretion detectably. Preliminary results also indicate that total quantities of at least one cuticular protein mRNA may increase during heat shock, either because of increased transcription or increased mRNA stability.

Molecular cloning and expression of a Tetrahymena pyriformis ubiquitin fusion gene coding for a 53-amino-acid extension protein

The genome of Tetrahymena pyriformis has been shown to contain a ubiquitin multigene family consisting of several polyubiquitin genes and at least one ubiquitin fusion gene. We report here the isolation and characterization of one genomic clone (pTU11), that encodes a ubiquitin extension protein. A comparison of the predicted amino acid sequence of the ubiquitin extension protein gene of T. pyriformis with those from other organisms indicated a high degree of homology. However, the Tetrahymena ubiquitin extension protein contains 53 and not 52 amino acids. This feature is different from all ubiquitin 52-amino-acid extension protein genes thus far sequenced. Furthermore, we found an array of four cysteine residues similar to those found in nucleic acid binding proteins. Also, the C-terminal sequence possesses a conserved motif which may represent a nuclear translocation signal. The ubiquitin 53-amino-acid extension protein gene encodes the smallest class of ubiquitin mRNAs in T. pyriformis.

The macronuclear polyubiquitin gene of the ciliate Tetrahymena pyriformis

The presence of ubiquitin in ciliates was first demonstrated in Tetrahymena pyriformis. One clone--pTU2--presents two incomplete open reading frames and the putative polyubiquitin genes have been shown to be highly similar to those of other organisms. To further analyze the organization of this multigene family, several fragments of macronuclear DNA were cloned. We report here the isolation and characterization of one genomic clone (pTU20) that encodes a polyubiquitin gene (TU20) with five tandem repeats and presenting only one extra triplet CAA (Gln) upstream from the TGA. The promoter region of TU20 also presents a consensus heat shock element. The specific detection of RNA species with a synthetic oligonucleotide probe reveals that it corresponds to the 1.8 kb mRNA species whose expression is increased by temperature stress.

Microbial stress proteins

There is general agreement that a function, perhaps the major function, of stress proteins under normal physiological conditions is to help assembly and disassembly of protein complexes and to catalyse protein-translocation processes. It remains unclear, however, as to what role these processes play in stressed cells. It could be that cells under stress produce abnormal, misfolded or otherwise damaged proteins and that increased synthesis of stress proteins is required to counter protein modifications. A role for stress proteins in recovery of cells from stress, as opposed to a role in helping cells to withstand a lethal stress, is thus suggested. The intracellular location of stress proteins, in the unstressed and stressed cell, is worthy of further studies. Members of the hsp70 family are associated with the cytosol, mitochondria and endoplasmic reticulum. There is evidence, particularly from studies on mammalian cells (Tanguay, 1985; Welch and Mizzen, 1988; Arrigo et al., 1988), that following stress hsps migrate to various cellular compartments and subsequently delocalize after stress. However, there is little comparable data from microbial systems for this phenomenon (e.g. Rossi and Lindquist, 1989). The question as to the role of stress proteins in the transient acquisition of thermotolerance remains to be answered. It is insufficient to equate the kinetics of stress-protein synthesis with acquisition of thermotolerance. Quantitative data on the amount of stress protein present at various times, including the recovery period, is required. The demonstration that microbial stress proteins are important antigenic determinants of micro-organisms causing major debilitating diseases in the world is an exciting observation. Studies on the interplay of pathogen and host, both carrying similar antigenic hsp determinants, will be a challenging area for future research. It is likely that E. coli and Sacch. cerevisiae, with their well-established biochemical and genetic properties, will continue to be the experimental systems of choice for studies on stress proteins. On the other hand, it is encouraging that studies on other micro-organisms have expanded in the past few years and have made substantial contributions towards our understanding of the stress response. The ubiquitous nature of the stress response and the remarkable evolutionary conservation of the stress proteins continue to be attractive areas for research.